diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8c103d7..614a624 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,49 @@ All notable changes to CmdForge will be documented in this file.
 
 ### Added
 
+#### System Dependencies
+- **System package dependencies for tools**: Tools can now declare system-level package dependencies (apt, brew, pacman, dnf)
+  - `system_dependencies` field in tool config.yaml
+  - Short form: just package name (e.g., `ffmpeg`)
+  - Long form: detailed spec with description, binaries to check, and per-manager package names
+  - Automatic platform detection (Linux/macOS/Windows)
+  - Package manager detection (apt, brew, pacman, dnf)
+
+- **New dataclass**: `SystemDependency` in tool.py
+  - `name` - Package identifier
+  - `description` - Why this dependency is needed
+  - `binaries` - List of executables to check (defaults to [name])
+  - `packages` - Package names per manager (defaults to name for all)
+  - Round-trip serialization preserves short/long form
+
+- **New module**: `src/cmdforge/system_deps.py`
+  - `detect_os()` - Returns 'linux', 'darwin', or 'windows'
+  - `detect_package_manager()` - Returns 'apt', 'brew', 'pacman', 'dnf', or None
+  - `check_system_dep()` - Check if dependency is satisfied (any binary found)
+  - `install_system_dep()` - Install via system package manager
+  - `prompt_install_missing()` - Interactive prompt for installing missing packages
+
+- **New CLI command**: `cmdforge system-deps <tool> [install]`
+  - `cmdforge system-deps <tool>` - Show system dependency status
+  - `cmdforge system-deps <tool> install` - Install missing system packages
+  - `--yes` flag for non-interactive installation
+
+- **Enhanced CLI commands**:
+  - `cmdforge check <tool>` - Now shows both CmdForge and system dependencies
+  - `cmdforge registry install` - Prompts to install system deps after tool install
+    - `--yes` flag to auto-install without prompting
+    - `--no-system-deps` flag to skip system dependency handling
+  - `cmdforge install` (project) - Handles system deps for manifest and lock-based installs
+
+- **GUI support**:
+  - Tool Builder: New "System Dependencies" section
+  - Add/Edit/Remove system dependency dialog
+  - Shows name and description in list
+
+- **Runtime integration**:
+  - Runner warns about missing system dependencies before execution
+  - Uses qualified tool refs (owner/name) for registry-installed tools
+
 #### Tool Settings Files
 - **Configurable tool settings**: Tools can now ship with default settings that users can customize
   - `defaults.yaml` - Default settings published with the tool (immutable)
diff --git a/src/cmdforge/cli/__init__.py b/src/cmdforge/cli/__init__.py
index cc903bf..c608afd 100644
--- a/src/cmdforge/cli/__init__.py
+++ b/src/cmdforge/cli/__init__.py
@@ -15,6 +15,7 @@ from .collections_commands import cmd_collections
 from .project_commands import cmd_deps, cmd_deps_tree, cmd_install_deps, cmd_add, cmd_remove, cmd_init, cmd_lock, cmd_verify
 from .config_commands import cmd_config
 from .settings_commands import cmd_settings
+from .system_deps_commands import cmd_system_deps
 
 
 def main():
@@ -163,6 +164,8 @@ def main():
     p_reg_install = registry_sub.add_parser("install", help="Install a tool from registry")
     p_reg_install.add_argument("tool", help="Tool to install (owner/name or name)")
     p_reg_install.add_argument("-v", "--version", help="Version constraint")
+    p_reg_install.add_argument("-y", "--yes", action="store_true", help="Auto-install system packages without prompting")
+    p_reg_install.add_argument("--no-system-deps", action="store_true", help="Skip system dependency check")
     p_reg_install.set_defaults(func=cmd_registry)
 
     # registry uninstall
@@ -397,6 +400,21 @@ def main():
     # Default for settings with no subcommand
     p_settings.set_defaults(func=cmd_settings)
 
+    # -------------------------------------------------------------------------
+    # System Dependencies Commands
+    # -------------------------------------------------------------------------
+    p_sysdeps = subparsers.add_parser("system-deps", help="Manage system package dependencies")
+    p_sysdeps.add_argument("tool", help="Tool name")
+    sysdeps_sub = p_sysdeps.add_subparsers(dest="system_deps_cmd")
+
+    # system-deps install
+    p_sysdeps_install = sysdeps_sub.add_parser("install", help="Install missing system packages")
+    p_sysdeps_install.add_argument("-y", "--yes", action="store_true", help="Install without prompting")
+    p_sysdeps_install.set_defaults(func=cmd_system_deps)
+
+    # Default for system-deps with no subcommand (show status)
+    p_sysdeps.set_defaults(func=cmd_system_deps)
+
     args = parser.parse_args()
 
     # If no command, launch UI
diff --git a/src/cmdforge/cli/project_commands.py b/src/cmdforge/cli/project_commands.py
index eb876ee..834b2fb 100644
--- a/src/cmdforge/cli/project_commands.py
+++ b/src/cmdforge/cli/project_commands.py
@@ -148,6 +148,7 @@ def cmd_install_deps(args):
     from ..resolver import ToolResolver, install_from_registry, ToolNotFoundError
     from ..registry_client import RegistryError
     from ..lockfile import Lockfile
+    from ..system_deps import prompt_install_missing
 
     manifest = load_manifest()
 
@@ -252,9 +253,13 @@ def cmd_install_deps(args):
             print(f"Installing {node.qualified_name}...", end=" ", flush=True)
             spec = node.qualified_name
             install_version = node.resolved_version or node.version_constraint
-            install_from_registry(spec, version=install_version)
+            resolved = install_from_registry(spec, version=install_version)
             print(f"v{node.resolved_version or 'latest'}")
             installed += 1
+            if resolved.tool.system_dependencies:
+                print()
+                tool_ref = f"{resolved.owner}/{resolved.tool.name}" if resolved.owner else resolved.tool.name
+                prompt_install_missing(resolved.tool.system_dependencies, tool_ref)
         except RegistryError as e:
             print(f"FAILED: {e.message}")
             failed.append((node.qualified_name, e.message))
@@ -278,6 +283,7 @@ def _install_from_lock(lock: "Lockfile", args) -> int:
     """Install exact versions from lock file."""
     from ..resolver import ToolResolver, ToolNotFoundError, install_from_registry
     from ..registry_client import RegistryError
+    from ..system_deps import prompt_install_missing
 
     verbose = getattr(args, 'verbose', False)
     dry_run = getattr(args, 'dry_run', False)
@@ -333,9 +339,13 @@ def _install_from_lock(lock: "Lockfile", args) -> int:
         try:
             print(f"Installing {pkg.name}@{pkg.version}...", end=" ", flush=True)
             # Use correct API: install_from_registry(spec, version)
-            install_from_registry(pkg.name, version=pkg.version)
+            resolved = install_from_registry(pkg.name, version=pkg.version)
             print("OK")
             installed += 1
+            if resolved.tool.system_dependencies:
+                print()
+                tool_ref = f"{resolved.owner}/{resolved.tool.name}" if resolved.owner else resolved.tool.name
+                prompt_install_missing(resolved.tool.system_dependencies, tool_ref)
         except RegistryError as e:
             print(f"FAILED: {e.message}")
             failed.append((pkg.name, e.message))
diff --git a/src/cmdforge/cli/registry_commands.py b/src/cmdforge/cli/registry_commands.py
index b69c490..a3dc349 100644
--- a/src/cmdforge/cli/registry_commands.py
+++ b/src/cmdforge/cli/registry_commands.py
@@ -190,9 +190,12 @@ def _cmd_registry_install(args):
     """Install a tool from the registry."""
     from ..registry_client import RegistryError
     from ..tool import BIN_DIR
+    from ..system_deps import prompt_install_missing
 
     tool_spec = args.tool
     version = args.version
+    auto_yes = getattr(args, 'yes', False)
+    skip_sys_deps = getattr(args, 'no_system_deps', False)
 
     print(f"Installing {tool_spec}...")
 
@@ -211,6 +214,12 @@ def _cmd_registry_install(args):
 
         print(f"\nRun with: {wrapper_name}")
 
+        # Check system dependencies unless skipped
+        if not skip_sys_deps and resolved.tool.system_dependencies:
+            print()
+            tool_ref = f"{resolved.owner}/{resolved.tool.name}" if resolved.owner else resolved.tool.name
+            prompt_install_missing(resolved.tool.system_dependencies, tool_ref, auto_yes=auto_yes)
+
     except RegistryError as e:
         if e.code == "TOOL_NOT_FOUND":
             print(f"Tool '{tool_spec}' not found in the registry.", file=sys.stderr)
diff --git a/src/cmdforge/cli/system_deps_commands.py b/src/cmdforge/cli/system_deps_commands.py
new file mode 100644
index 0000000..ef507da
--- /dev/null
+++ b/src/cmdforge/cli/system_deps_commands.py
@@ -0,0 +1,141 @@
+"""System dependencies commands."""
+
+import sys
+
+from ..tool import load_tool
+from ..system_deps import (
+    detect_os, detect_package_manager,
+    check_and_report, format_dep_status,
+    install_system_dep, get_install_command_string
+)
+
+
+def cmd_system_deps(args):
+    """Handle system-deps subcommands."""
+    tool_name = args.tool
+
+    tool = load_tool(tool_name)
+    if not tool:
+        print(f"Error: Tool '{tool_name}' not found.", file=sys.stderr)
+        return 1
+
+    if not tool.system_dependencies:
+        print(f"Tool '{tool_name}' has no system dependencies declared.")
+        return 0
+
+    subcmd = getattr(args, 'system_deps_cmd', None)
+
+    if subcmd == "install":
+        return _cmd_install(args, tool)
+    else:
+        # Default: show status
+        return _cmd_status(args, tool)
+
+
+def _cmd_status(args, tool):
+    """Show system dependency status for a tool."""
+    print(f"System Dependencies for '{tool.name}':")
+    print()
+
+    pkg_manager = detect_package_manager()
+    installed, missing = check_and_report(tool.system_dependencies)
+
+    for dep in tool.system_dependencies:
+        status = format_dep_status(dep, pkg_manager if dep in missing else None)
+        print(status)
+
+    print()
+
+    if missing:
+        if pkg_manager:
+            print(f"Package manager: {pkg_manager}")
+            print(f"Install missing with: cmdforge system-deps {tool.name} install")
+        else:
+            os_type = detect_os()
+            if os_type == "windows":
+                print("Note: Automatic installation not supported on Windows.")
+                print("Please install the packages manually.")
+            else:
+                print("Warning: No supported package manager found.")
+        return 1
+    else:
+        print("All system dependencies satisfied.")
+        return 0
+
+
+def _cmd_install(args, tool):
+    """Install missing system dependencies."""
+    os_type = detect_os()
+
+    if os_type == "windows":
+        print("Automatic installation not supported on Windows.", file=sys.stderr)
+        print()
+        print("Please install these packages manually:")
+        for dep in tool.system_dependencies:
+            print(f"  - {dep.name}")
+            if dep.description:
+                print(f"    {dep.description}")
+        return 1
+
+    pkg_manager = detect_package_manager()
+    if not pkg_manager:
+        print("Error: No supported package manager found.", file=sys.stderr)
+        print("Supported: apt, brew, pacman, dnf", file=sys.stderr)
+        return 1
+
+    installed, missing = check_and_report(tool.system_dependencies)
+
+    if not missing:
+        print("All system dependencies are already installed.")
+        return 0
+
+    print(f"Missing system packages ({len(missing)}):")
+    for dep in missing:
+        desc = f" - {dep.description}" if dep.description else ""
+        print(f"  {dep.name}{desc}")
+        print(f"    Install: {get_install_command_string(dep, pkg_manager)}")
+    print()
+
+    # Check for --yes flag
+    auto_yes = getattr(args, 'yes', False)
+
+    if not auto_yes:
+        try:
+            confirm = input(f"Install {len(missing)} package(s)? [Y/n] ")
+            if confirm.lower() not in ('', 'y', 'yes'):
+                print("Cancelled.")
+                return 0
+        except (EOFError, KeyboardInterrupt):
+            print("\nCancelled.")
+            return 0
+
+    print()
+    print(f"Installing packages with {pkg_manager}...")
+    print()
+
+    # Track results
+    succeeded = []
+    failed = []
+
+    for dep in missing:
+        print(f"Installing {dep.name}...")
+        success, msg = install_system_dep(dep, pkg_manager)
+        if success:
+            print(f"  \u2713 {msg}")
+            succeeded.append(dep)
+        else:
+            print(f"  \u2717 {msg}")
+            failed.append((dep, msg))
+
+    print()
+
+    if failed:
+        print(f"Installed {len(succeeded)}/{len(missing)} packages.")
+        print()
+        print("Failed packages:")
+        for dep, msg in failed:
+            print(f"  {dep.name}: {msg}")
+        return 1
+    else:
+        print(f"Successfully installed {len(succeeded)} package(s).")
+        return 0
diff --git a/src/cmdforge/cli/tool_commands.py b/src/cmdforge/cli/tool_commands.py
index 675b1f4..ce10945 100644
--- a/src/cmdforge/cli/tool_commands.py
+++ b/src/cmdforge/cli/tool_commands.py
@@ -5,7 +5,7 @@ from pathlib import Path
 
 from ..tool import (
     list_tools, load_tool, save_tool, delete_tool, get_tools_dir,
-    Tool, ToolArgument, PromptStep, CodeStep, ToolStep
+    Tool, ToolArgument, PromptStep, CodeStep, ToolStep, validate_tool_name
 )
 from ..gui import run_gui
 
@@ -59,6 +59,12 @@ def cmd_create(args):
     """Create a new tool (basic CLI creation - use 'ui' for full builder)."""
     name = args.name
 
+    # Validate tool name
+    is_valid, error_msg = validate_tool_name(name)
+    if not is_valid:
+        print(f"Error: Invalid tool name '{name}': {error_msg}")
+        return 1
+
     # Check if already exists
     existing = load_tool(name)
     if existing and not args.force:
@@ -223,29 +229,58 @@ def cmd_run(args):
         if tool_args and tool_args[0] == '--':
             tool_args = tool_args[1:]
 
+        def is_flag(s: str) -> bool:
+            """Check if string looks like a flag (not a negative number)."""
+            if not s.startswith('-'):
+                return False
+            # Check if it's a negative number (e.g., -5, -3.14)
+            rest = s[1:] if s.startswith('--') else s[1:]
+            if s.startswith('--'):
+                rest = s[2:]
+            try:
+                float(rest)
+                return False  # It's a negative number, not a flag
+            except ValueError:
+                return True  # It's a flag
+
         # Parse tool-specific arguments
         i = 0
         while i < len(tool_args):
             arg = tool_args[i]
             if arg.startswith('--'):
-                flag_key = arg[2:].replace('-', '_')
-                # Map flag name to variable name (use flag_key as fallback for unknown flags)
-                var_name = flag_to_var.get(flag_key, flag_key)
-                if i + 1 < len(tool_args) and not tool_args[i + 1].startswith('--'):
-                    custom_args[var_name] = tool_args[i + 1]
-                    i += 2
-                else:
-                    custom_args[var_name] = True
+                # Handle --flag=value syntax
+                if '=' in arg:
+                    flag_part, value = arg.split('=', 1)
+                    flag_key = flag_part[2:].replace('-', '_')
+                    var_name = flag_to_var.get(flag_key, flag_key)
+                    custom_args[var_name] = value
                     i += 1
-            elif arg.startswith('-'):
-                flag_key = arg[1:].replace('-', '_')
-                var_name = flag_to_var.get(flag_key, flag_key)
-                if i + 1 < len(tool_args) and not tool_args[i + 1].startswith('-'):
-                    custom_args[var_name] = tool_args[i + 1]
-                    i += 2
                 else:
-                    custom_args[var_name] = True
+                    flag_key = arg[2:].replace('-', '_')
+                    var_name = flag_to_var.get(flag_key, flag_key)
+                    if i + 1 < len(tool_args) and not is_flag(tool_args[i + 1]):
+                        custom_args[var_name] = tool_args[i + 1]
+                        i += 2
+                    else:
+                        custom_args[var_name] = True
+                        i += 1
+            elif arg.startswith('-') and is_flag(arg):
+                # Handle -f=value syntax
+                if '=' in arg:
+                    flag_part, value = arg.split('=', 1)
+                    flag_key = flag_part[1:].replace('-', '_')
+                    var_name = flag_to_var.get(flag_key, flag_key)
+                    custom_args[var_name] = value
                     i += 1
+                else:
+                    flag_key = arg[1:].replace('-', '_')
+                    var_name = flag_to_var.get(flag_key, flag_key)
+                    if i + 1 < len(tool_args) and not is_flag(tool_args[i + 1]):
+                        custom_args[var_name] = tool_args[i + 1]
+                        i += 2
+                    else:
+                        custom_args[var_name] = True
+                        i += 1
             else:
                 i += 1
 
@@ -365,52 +400,89 @@ echo "input" | {args.name}
 
 
 def cmd_check(args):
-    """Check dependencies for a tool (meta-tools)."""
+    """Check dependencies for a tool (meta-tools and system packages)."""
     from ..runner import check_dependencies
     from ..tool import ToolStep
+    from ..system_deps import (
+        check_and_report, detect_package_manager, format_dep_status
+    )
 
     tool = load_tool(args.name)
     if not tool:
         print(f"Error: Tool '{args.name}' not found.")
         return 1
 
+    print(f"Tool: {args.name}")
+    print()
+
+    has_issues = False
+
     # Check if this is a meta-tool
     has_tool_steps = any(isinstance(s, ToolStep) for s in tool.steps)
     has_deps = bool(tool.dependencies)
+    has_sys_deps = bool(tool.system_dependencies)
 
-    if not has_tool_steps and not has_deps:
-        print(f"Tool '{args.name}' has no dependencies (not a meta-tool).")
+    # CmdForge Dependencies section
+    if has_deps or has_tool_steps:
+        print("CmdForge Dependencies:")
+
+        # Show declared dependencies
+        if tool.dependencies:
+            missing = check_dependencies(tool)
+            for dep in tool.dependencies:
+                if dep in missing:
+                    print(f"  \u2717 {dep} (not installed)")
+                else:
+                    print(f"  \u2713 {dep} (installed)")
+
+        # Show tool steps
+        if has_tool_steps:
+            for i, step in enumerate(tool.steps):
+                if isinstance(step, ToolStep):
+                    # Check if already shown as explicit dependency
+                    if step.tool not in (tool.dependencies or []):
+                        from ..resolver import resolve_tool, ToolNotFoundError
+                        try:
+                            resolve_tool(step.tool)
+                            print(f"  \u2713 {step.tool} (step {i+1}, installed)")
+                        except ToolNotFoundError:
+                            print(f"  \u2717 {step.tool} (step {i+1}, not installed)")
+
+        # Check which are missing
+        missing = check_dependencies(tool)
+        if missing:
+            has_issues = True
+            print()
+            print(f"  Install missing tools with:")
+            print(f"    cmdforge install {' '.join(missing)}")
+
+        print()
+
+    # System Dependencies section
+    if has_sys_deps:
+        print("System Dependencies:")
+        pkg_manager = detect_package_manager()
+
+        installed, missing = check_and_report(tool.system_dependencies)
+
+        for dep in tool.system_dependencies:
+            status = format_dep_status(dep, pkg_manager if dep in missing else None)
+            print(status)
+
+        if missing:
+            has_issues = True
+            print()
+            print(f"  Install missing packages with:")
+            print(f"    cmdforge system-deps {args.name} install")
+
+        print()
+
+    if not has_deps and not has_tool_steps and not has_sys_deps:
+        print("No dependencies declared.")
         return 0
 
-    print(f"Checking dependencies for '{args.name}'...")
-    print()
-
-    # Show declared dependencies
-    if tool.dependencies:
-        print("Declared dependencies:")
-        for dep in tool.dependencies:
-            print(f"  - {dep}")
-        print()
-
-    # Show tool steps
-    if has_tool_steps:
-        print("Tool steps (implicit dependencies):")
-        for i, step in enumerate(tool.steps):
-            if isinstance(step, ToolStep):
-                print(f"  Step {i+1}: {step.tool}")
-        print()
-
-    # Check which are missing
-    missing = check_dependencies(tool)
-
-    if missing:
-        print(f"Missing dependencies ({len(missing)}):")
-        for dep in missing:
-            print(f"  - {dep}")
-        print()
-        print("Install with:")
-        print(f"  cmdforge install {' '.join(missing)}")
+    if has_issues:
         return 1
     else:
-        print("All dependencies are satisfied.")
+        print("All dependencies satisfied.")
         return 0
diff --git a/src/cmdforge/gui/dialogs/system_dep_dialog.py b/src/cmdforge/gui/dialogs/system_dep_dialog.py
new file mode 100644
index 0000000..75ef30f
--- /dev/null
+++ b/src/cmdforge/gui/dialogs/system_dep_dialog.py
@@ -0,0 +1,159 @@
+"""System dependency editor dialog."""
+
+from PySide6.QtWidgets import (
+    QDialog, QVBoxLayout, QFormLayout, QLineEdit,
+    QPushButton, QHBoxLayout, QLabel, QGroupBox
+)
+
+from ...tool import SystemDependency
+
+
+class SystemDependencyDialog(QDialog):
+    """Dialog for editing system dependencies."""
+
+    def __init__(self, parent, dep: SystemDependency = None):
+        super().__init__(parent)
+        self.setWindowTitle("Edit System Dependency" if dep else "Add System Dependency")
+        self.setMinimumWidth(450)
+        self._dep = dep
+        self._setup_ui()
+
+        if dep:
+            self._load_dep(dep)
+
+    def _setup_ui(self):
+        """Set up the UI."""
+        layout = QVBoxLayout(self)
+        layout.setSpacing(16)
+
+        # Basic info
+        form = QFormLayout()
+        form.setSpacing(12)
+
+        self.name_input = QLineEdit()
+        self.name_input.setPlaceholderText("ffmpeg")
+        self.name_input.setToolTip("Package name (used as default for all package managers)")
+        form.addRow("Name:", self.name_input)
+
+        self.desc_input = QLineEdit()
+        self.desc_input.setPlaceholderText("Audio/video processing (optional)")
+        self.desc_input.setToolTip("Human-readable description of why this package is needed")
+        form.addRow("Description:", self.desc_input)
+
+        self.binaries_input = QLineEdit()
+        self.binaries_input.setPlaceholderText("ffplay, ffmpeg (optional, comma-separated)")
+        self.binaries_input.setToolTip(
+            "Executables to check for. If any exist, dependency is satisfied.\n"
+            "Leave empty to check for the package name itself."
+        )
+        form.addRow("Binaries:", self.binaries_input)
+
+        layout.addLayout(form)
+
+        # Package names (advanced)
+        pkg_group = QGroupBox("Package Names (Advanced)")
+        pkg_group.setToolTip("Override package name for specific package managers")
+        pkg_layout = QFormLayout(pkg_group)
+        pkg_layout.setSpacing(8)
+
+        self.apt_input = QLineEdit()
+        self.apt_input.setPlaceholderText("(uses name if empty)")
+        pkg_layout.addRow("apt:", self.apt_input)
+
+        self.brew_input = QLineEdit()
+        self.brew_input.setPlaceholderText("(uses name if empty)")
+        pkg_layout.addRow("brew:", self.brew_input)
+
+        self.pacman_input = QLineEdit()
+        self.pacman_input.setPlaceholderText("(uses name if empty)")
+        pkg_layout.addRow("pacman:", self.pacman_input)
+
+        self.dnf_input = QLineEdit()
+        self.dnf_input.setPlaceholderText("(uses name if empty)")
+        pkg_layout.addRow("dnf:", self.dnf_input)
+
+        layout.addWidget(pkg_group)
+
+        # Help text
+        help_text = QLabel(
+            "System dependencies are installed via the system package manager\n"
+            "(apt, brew, pacman, dnf). Users will be prompted to install missing\n"
+            "packages when they install your tool from the registry."
+        )
+        help_text.setStyleSheet("color: #718096; font-size: 11px;")
+        help_text.setWordWrap(True)
+        layout.addWidget(help_text)
+
+        # Buttons
+        buttons = QHBoxLayout()
+        buttons.addStretch()
+
+        self.btn_cancel = QPushButton("Cancel")
+        self.btn_cancel.setObjectName("secondary")
+        self.btn_cancel.clicked.connect(self.reject)
+        buttons.addWidget(self.btn_cancel)
+
+        self.btn_ok = QPushButton("OK")
+        self.btn_ok.clicked.connect(self._validate_and_accept)
+        buttons.addWidget(self.btn_ok)
+
+        layout.addLayout(buttons)
+
+    def _load_dep(self, dep: SystemDependency):
+        """Load dependency data into form."""
+        self.name_input.setText(dep.name)
+        self.desc_input.setText(dep.description or "")
+
+        if dep.binaries:
+            self.binaries_input.setText(", ".join(dep.binaries))
+
+        # Package overrides
+        if dep.packages:
+            self.apt_input.setText(dep.packages.get("apt", ""))
+            self.brew_input.setText(dep.packages.get("brew", ""))
+            self.pacman_input.setText(dep.packages.get("pacman", ""))
+            self.dnf_input.setText(dep.packages.get("dnf", ""))
+
+    def _validate_and_accept(self):
+        """Validate input and accept."""
+        name = self.name_input.text().strip()
+
+        if not name:
+            self.name_input.setFocus()
+            return
+
+        self.accept()
+
+    def get_dependency(self) -> SystemDependency:
+        """Get the dependency from form data."""
+        name = self.name_input.text().strip()
+        description = self.desc_input.text().strip()
+
+        # Parse binaries
+        binaries_text = self.binaries_input.text().strip()
+        binaries = []
+        if binaries_text:
+            binaries = [b.strip() for b in binaries_text.split(",") if b.strip()]
+
+        # Collect package overrides (only non-empty values)
+        packages = {}
+        if self.apt_input.text().strip():
+            packages["apt"] = self.apt_input.text().strip()
+        if self.brew_input.text().strip():
+            packages["brew"] = self.brew_input.text().strip()
+        if self.pacman_input.text().strip():
+            packages["pacman"] = self.pacman_input.text().strip()
+        if self.dnf_input.text().strip():
+            packages["dnf"] = self.dnf_input.text().strip()
+
+        # Determine original format for round-trip serialization
+        # Use short form if only name is provided
+        original_format = "short" if (not description and not binaries and not packages) else "long"
+
+        return SystemDependency(
+            name=name,
+            description=description,
+            binaries=binaries,
+            packages=packages,
+            _original_format=original_format
+        )
diff --git a/src/cmdforge/gui/pages/tool_builder_page.py b/src/cmdforge/gui/pages/tool_builder_page.py
index 47ab1da..d289103 100644
--- a/src/cmdforge/gui/pages/tool_builder_page.py
+++ b/src/cmdforge/gui/pages/tool_builder_page.py
@@ -177,6 +177,49 @@ class ToolBuilderPage(QWidget):
 
         left_layout.addWidget(deps_box)
 
+        # System Dependencies group (compact)
+        sys_deps_box = QGroupBox()
+        sys_deps_layout = QVBoxLayout(sys_deps_box)
+        sys_deps_layout.setContentsMargins(9, 9, 9, 9)
+        sys_deps_layout.setSpacing(8)
+
+        sys_deps_label = QLabel("System Dependencies")
+        sys_deps_label.setObjectName("sectionHeading")
+        sys_deps_label.setToolTip(
+            "System packages (apt, brew, pacman, dnf) required by your tool.\n"
+            "Users will be prompted to install missing packages."
+        )
+        sys_deps_layout.addWidget(sys_deps_label)
+
+        self.sys_deps_list = QListWidget()
+        self.sys_deps_list.setMaximumHeight(80)
+        self.sys_deps_list.setMinimumHeight(60)
+        self.sys_deps_list.itemDoubleClicked.connect(self._edit_sys_dep)
+        sys_deps_layout.addWidget(self.sys_deps_list)
+
+        # System dependency buttons
+        sys_deps_btns = QHBoxLayout()
+        sys_deps_btns.setSpacing(6)
+
+        self.btn_add_sys_dep = QPushButton("Add")
+        self.btn_add_sys_dep.clicked.connect(self._add_sys_dep)
+        sys_deps_btns.addWidget(self.btn_add_sys_dep)
+
+        self.btn_edit_sys_dep = QPushButton("Edit")
+        self.btn_edit_sys_dep.setObjectName("secondary")
+        self.btn_edit_sys_dep.clicked.connect(self._edit_sys_dep)
+        sys_deps_btns.addWidget(self.btn_edit_sys_dep)
+
+        self.btn_del_sys_dep = QPushButton("Remove")
+        self.btn_del_sys_dep.setObjectName("danger")
+        self.btn_del_sys_dep.clicked.connect(self._delete_sys_dep)
+        sys_deps_btns.addWidget(self.btn_del_sys_dep)
+
+        sys_deps_btns.addStretch()
+        sys_deps_layout.addLayout(sys_deps_btns)
+
+        left_layout.addWidget(sys_deps_box)
+
         # Defaults group (collapsible)
         self.defaults_group = QGroupBox("Defaults (Optional)")
         self.defaults_group.setCheckable(True)
@@ -484,6 +527,9 @@ class ToolBuilderPage(QWidget):
         # Load dependencies
         self._refresh_dependencies()
 
+        # Load system dependencies
+        self._refresh_sys_deps()
+
         # Load steps
         self._refresh_steps()
 
@@ -727,6 +773,68 @@ class ToolBuilderPage(QWidget):
             for dep in self._tool.dependencies:
                 self.deps_list.addItem(dep)
 
+    def _add_sys_dep(self):
+        """Add a new system dependency."""
+        from ..dialogs.system_dep_dialog import SystemDependencyDialog
+        dialog = SystemDependencyDialog(self)
+        if dialog.exec():
+            dep = dialog.get_dependency()
+            if not self._tool:
+                from ...tool import Tool
+                self._tool = Tool(name="", description="")
+            if not hasattr(self._tool, 'system_dependencies') or self._tool.system_dependencies is None:
+                self._tool.system_dependencies = []
+
+            # Check if already exists
+            existing_names = [d.name for d in self._tool.system_dependencies]
+            if dep.name in existing_names:
+                self.main_window.show_status(f"'{dep.name}' is already a system dependency")
+                return
+
+            self._tool.system_dependencies.append(dep)
+            self._refresh_sys_deps()
+            self.main_window.show_status(f"Added system dependency: {dep.name}")
+
+    def _edit_sys_dep(self):
+        """Edit selected system dependency."""
+        items = self.sys_deps_list.selectedItems()
+        if not items:
+            return
+
+        idx = self.sys_deps_list.row(items[0])
+        if not self._tool or idx >= len(self._tool.system_dependencies):
+            return
+
+        dep = self._tool.system_dependencies[idx]
+
+        from ..dialogs.system_dep_dialog import SystemDependencyDialog
+        dialog = SystemDependencyDialog(self, dep)
+        if dialog.exec():
+            self._tool.system_dependencies[idx] = dialog.get_dependency()
+            self._refresh_sys_deps()
+
+    def _delete_sys_dep(self):
+        """Remove selected system dependency."""
+        items = self.sys_deps_list.selectedItems()
+        if not items:
+            return
+
+        idx = self.sys_deps_list.row(items[0])
+        if self._tool and self._tool.system_dependencies and idx < len(self._tool.system_dependencies):
+            del self._tool.system_dependencies[idx]
+            self._refresh_sys_deps()
+
+    def _refresh_sys_deps(self):
+        """Refresh system dependencies list widget."""
+        self.sys_deps_list.clear()
+        if self._tool and self._tool.system_dependencies:
+            for dep in self._tool.system_dependencies:
+                # Show name and description if available
+                text = dep.name
+                if dep.description:
+                    text += f" - {dep.description}"
+                self.sys_deps_list.addItem(text)
+
     def _add_tool_dependency(self, tool_ref: str):
         """Add a tool reference to the dependencies list if not already present.
 
@@ -979,7 +1087,8 @@ class ToolBuilderPage(QWidget):
             arguments=self._tool.arguments if self._tool else [],
             steps=self._tool.steps if self._tool else [],
             output=output,
-            dependencies=self._tool.dependencies if self._tool else []
+            dependencies=self._tool.dependencies if self._tool else [],
+            system_dependencies=self._tool.system_dependencies if self._tool else []
         )
 
         # Preserve source if editing
diff --git a/src/cmdforge/resolver.py b/src/cmdforge/resolver.py
index ed0594e..44dd023 100644
--- a/src/cmdforge/resolver.py
+++ b/src/cmdforge/resolver.py
@@ -467,7 +467,7 @@ class ToolResolver:
         script = f"""#!/bin/bash
 # CmdForge wrapper for '{owner}/{name}'
 # Auto-generated - do not edit
-exec {python_path} -m cmdforge.runner {owner}/{name} "$@"
+exec "{python_path}" -m cmdforge.runner "{owner}/{name}" "$@"
 """
 
         wrapper_path.write_text(script)
diff --git a/src/cmdforge/runner.py b/src/cmdforge/runner.py
index 96b2f4e..58df4b6 100644
--- a/src/cmdforge/runner.py
+++ b/src/cmdforge/runner.py
@@ -17,6 +17,24 @@ from .profiles import load_profile
 MAX_TOOL_DEPTH = 10
 
 
+def check_system_dependencies(tool: Tool) -> list:
+    """
+    Check if system dependencies are satisfied.
+
+    Args:
+        tool: Tool to check system dependencies for
+
+    Returns:
+        List of missing SystemDependency objects
+    """
+    from .system_deps import check_system_dep
+
+    if not tool.system_dependencies:
+        return []
+
+    return [d for d in tool.system_dependencies if not check_system_dep(d)]
+
+
 def auto_install_dependencies(tool: Tool, verbose: bool = False) -> list[str]:
     """
     Automatically install missing dependencies for a tool.
@@ -155,7 +173,8 @@ def substitute_variables(template: str, variables: dict, warn_non_scalar: bool =
     for name, value in variables.items():
         if name == "settings":
             continue  # Already handled above
-        result = result.replace(f"{{{name}}}", str(value) if value else "")
+        # Use 'is not None' to preserve falsey values like 0 and False
+        result = result.replace(f"{{{name}}}", "" if value is None else str(value))
 
     # Finally, restore escaped braces as single braces
     result = result.replace(ESCAPE_OPEN, "{").replace(ESCAPE_CLOSE, "}")
@@ -236,7 +255,9 @@ def execute_code_step(
         output_vars = [v.strip() for v in step.output_var.split(',')]
         outputs = {}
         for var in output_vars:
-            outputs[var] = str(local_vars.get(var, ""))
+            # Preserve original types for code→code workflows
+            # Template substitution will convert to string when needed
+            outputs[var] = local_vars.get(var)
 
         return outputs, True
 
@@ -388,6 +409,17 @@ def run_tool(
     Returns:
         Tuple of (output_text, exit_code)
     """
+    def _format_tool_ref(current_tool: Tool) -> str:
+        """Best-effort tool reference for messages (owner/name if available)."""
+        if current_tool.path:
+            tool_dir = current_tool.path.parent
+            # Handle both global and local ~/.cmdforge/<owner>/<name> layouts
+            if tool_dir.parent.name == ".cmdforge":
+                return tool_dir.name
+            if tool_dir.parent.parent.name == ".cmdforge":
+                return f"{tool_dir.parent.name}/{tool_dir.name}"
+        return current_tool.name
+
     # Initialize call stack
     if _call_stack is None:
         _call_stack = []
@@ -412,6 +444,15 @@ def run_tool(
                 print(f"Or use --auto-install to install automatically", file=sys.stderr)
             # Continue anyway - the actual step execution will fail with a better error
 
+    # Check system dependencies on first level only
+    if _depth == 0 and tool.system_dependencies:
+        missing_sys = check_system_dependencies(tool)
+        if missing_sys:
+            names = ", ".join(d.name for d in missing_sys)
+            print(f"Warning: Missing system packages: {names}", file=sys.stderr)
+            print(f"Run: cmdforge system-deps {_format_tool_ref(tool)} install", file=sys.stderr)
+            # Continue execution - let it fail naturally if dep is actually needed
+
     # Initialize variables with input and arguments
     variables = {"input": input_text}
 
diff --git a/src/cmdforge/system_deps.py b/src/cmdforge/system_deps.py
new file mode 100644
index 0000000..eb740e7
--- /dev/null
+++ b/src/cmdforge/system_deps.py
@@ -0,0 +1,313 @@
+"""System dependency management.
+
+Handles detection, checking, and installation of system-level package
+dependencies (apt, brew, pacman, dnf) for CmdForge tools.
+"""
+
+import platform
+import shutil
+import subprocess
+import sys
+from typing import Optional, List, Tuple, TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from .tool import SystemDependency
+
+# Supported package managers in precedence order
+SUPPORTED_MANAGERS = ["apt", "brew", "pacman", "dnf"]
+
+
+def detect_os() -> str:
+    """Detect operating system.
+
+    Returns:
+        'linux', 'darwin', or 'windows'
+    """
+    system = platform.system().lower()
+    if system == "darwin":
+        return "darwin"
+    elif system == "windows":
+        return "windows"
+    return "linux"
+
+
+def detect_package_manager() -> Optional[str]:
+    """Detect the system's package manager.
+
+    Uses shutil.which for fast detection without subprocess overhead.
+
+    Returns:
+        Package manager name ('apt', 'brew', 'pacman', 'dnf') or None
+    """
+    os_type = detect_os()
+
+    if os_type == "windows":
+        return None  # Windows not supported for auto-install
+
+    # Manager binary names (apt uses apt-get for scripted installs)
+    manager_binaries = {
+        "apt": "apt-get",
+        "brew": "brew",
+        "pacman": "pacman",
+        "dnf": "dnf",
+    }
+
+    # On macOS, check brew first
+    if os_type == "darwin":
+        if shutil.which("brew"):
+            return "brew"
+        return None
+
+    # On Linux, check in order of preference
+    for manager, binary in manager_binaries.items():
+        if shutil.which(binary):
+            return manager
+
+    return None
+
+
+def check_system_dep(dep: "SystemDependency") -> bool:
+    """Check if a system dependency is installed.
+
+    A dependency is considered satisfied if ANY of its binaries exist.
+
+    Args:
+        dep: SystemDependency to check
+
+    Returns:
+        True if dependency is satisfied (at least one binary found)
+    """
+    binaries = dep.get_binaries_to_check()
+    return any(shutil.which(b) is not None for b in binaries)
+
+
+def get_binary_path(dep: "SystemDependency") -> Optional[str]:
+    """Get the path to the first found binary for a dependency.
+
+    Args:
+        dep: SystemDependency to check
+
+    Returns:
+        Path to binary, or None if not found
+    """
+    binaries = dep.get_binaries_to_check()
+    for b in binaries:
+        path = shutil.which(b)
+        if path:
+            return path
+    return None
+
+
+def get_install_command(dep: "SystemDependency", pkg_manager: str) -> Optional[List[str]]:
+    """Get the install command as a list (safe, no shell injection).
+
+    Args:
+        dep: SystemDependency to install
+        pkg_manager: Package manager to use ('apt', 'brew', 'pacman', 'dnf')
+
+    Returns:
+        Command as list of strings, or None if unsupported manager
+    """
+    pkg_name = dep.get_package_name(pkg_manager)
+
+    commands = {
+        "apt": ["sudo", "apt-get", "install", "-y", pkg_name],
+        "brew": ["brew", "install", pkg_name],
+        "pacman": ["sudo", "pacman", "-S", "--noconfirm", pkg_name],
+        "dnf": ["sudo", "dnf", "install", "-y", pkg_name],
+    }
+    return commands.get(pkg_manager)
+
+
+def get_install_command_string(dep: "SystemDependency", pkg_manager: str) -> str:
+    """Get human-readable install command for display.
+
+    Args:
+        dep: SystemDependency to install
+        pkg_manager: Package manager to use
+
+    Returns:
+        Command as string for display to user
+    """
+    cmd = get_install_command(dep, pkg_manager)
+    return " ".join(cmd) if cmd else f"# No install command for {pkg_manager}"
+
+
+def install_system_dep(dep: "SystemDependency", pkg_manager: str) -> Tuple[bool, str]:
+    """Install a system dependency.
+
+    Args:
+        dep: SystemDependency to install
+        pkg_manager: Package manager to use
+
+    Returns:
+        Tuple of (success, message)
+    """
+    cmd = get_install_command(dep, pkg_manager)
+    if not cmd:
+        return False, f"No install command for package manager: {pkg_manager}"
+
+    try:
+        result = subprocess.run(cmd, capture_output=True, text=True)
+        if result.returncode == 0:
+            # Verify installation worked
+            if check_system_dep(dep):
+                return True, f"Installed {dep.name}"
+            else:
+                return False, f"Installed but binaries not found"
+        else:
+            error = result.stderr.strip() or result.stdout.strip()
+            return False, f"Failed: {error[:200]}"
+    except FileNotFoundError:
+        return False, f"Package manager '{pkg_manager}' not found"
+    except PermissionError:
+        return False, "Permission denied (try running with sudo)"
+    except Exception as e:
+        return False, str(e)
+
+
+def check_and_report(deps: List["SystemDependency"]) -> Tuple[List["SystemDependency"], List["SystemDependency"]]:
+    """Check dependencies and return categorized lists.
+
+    Args:
+        deps: List of SystemDependency objects to check
+
+    Returns:
+        Tuple of (installed_deps, missing_deps)
+    """
+    installed = []
+    missing = []
+    for dep in deps:
+        if check_system_dep(dep):
+            installed.append(dep)
+        else:
+            missing.append(dep)
+    return installed, missing
+
+
+def format_dep_status(dep: "SystemDependency", pkg_manager: Optional[str] = None) -> str:
+    """Format dependency status for display.
+
+    Args:
+        dep: SystemDependency to format
+        pkg_manager: Optional package manager for install hint
+
+    Returns:
+        Formatted status string
+    """
+    if check_system_dep(dep):
+        path = get_binary_path(dep)
+        return f"  \u2713 {dep.name} (found: {path})"
+    else:
+        binaries = dep.get_binaries_to_check()
+        line = f"  \u2717 {dep.name} (not found"
+        if len(binaries) > 1:
+            line += f", provides: {', '.join(binaries)}"
+        line += ")"
+        if pkg_manager:
+            install_cmd = get_install_command_string(dep, pkg_manager)
+            line += f"\n    Install: {install_cmd}"
+        return line
+
+
+def install_missing_deps(
+    deps: List["SystemDependency"],
+    pkg_manager: str,
+    callback=None
+) -> List[Tuple["SystemDependency", bool, str]]:
+    """Install multiple missing dependencies.
+
+    Args:
+        deps: List of SystemDependency objects to install
+        pkg_manager: Package manager to use
+        callback: Optional callback(dep, success, message) called after each install
+
+    Returns:
+        List of tuples: (dep, success, message)
+    """
+    results = []
+    for dep in deps:
+        success, msg = install_system_dep(dep, pkg_manager)
+        results.append((dep, success, msg))
+        if callback:
+            callback(dep, success, msg)
+    return results
+
+
+def prompt_install_missing(
+    deps: List["SystemDependency"],
+    tool_ref: str,
+    auto_yes: bool = False
+) -> None:
+    """Prompt to install missing system dependencies for a tool.
+
+    Args:
+        deps: List of system dependencies.
+        tool_ref: Tool reference string for messages (owner/name or name).
+        auto_yes: If True, install without prompting.
+    """
+    installed, missing = check_and_report(deps)
+    if not missing:
+        return
+
+    print(f"Tool '{tool_ref}' requires system packages:")
+    pkg_manager = detect_package_manager()
+
+    for dep in missing:
+        desc = f" - {dep.description}" if dep.description else ""
+        print(f"  \u2717 {dep.name}{desc}")
+        if pkg_manager:
+            print(f"    Install: {get_install_command_string(dep, pkg_manager)}")
+
+    print()
+
+    os_type = detect_os()
+    if os_type == "windows":
+        print("Note: Automatic installation not supported on Windows.")
+        print("Please install the packages manually.")
+        return
+
+    if not pkg_manager:
+        print("Warning: No supported package manager found.")
+        print("Please install the packages manually.")
+        return
+
+    if not auto_yes and not sys.stdin.isatty():
+        print("Skipping system package install (non-interactive).")
+        print(f"Install later with: cmdforge system-deps {tool_ref} install")
+        return
+
+    if auto_yes:
+        do_install = True
+    else:
+        try:
+            confirm = input(f"Install {len(missing)} missing package(s)? [Y/n] ")
+            do_install = confirm.lower() in ('', 'y', 'yes')
+        except (EOFError, KeyboardInterrupt):
+            print("\nSkipping system package installation.")
+            return
+
+    if not do_install:
+        print(f"Skipped. Install later with: cmdforge system-deps {tool_ref} install")
+        return
+
+    print()
+    succeeded = 0
+    failed = 0
+
+    for dep in missing:
+        print(f"Installing {dep.name}...")
+        success, msg = install_system_dep(dep, pkg_manager)
+        if success:
+            print(f"  \u2713 {msg}")
+            succeeded += 1
+        else:
+            print(f"  \u2717 {msg}")
+            failed += 1
+
+    print()
+    if failed:
+        print(f"Installed {succeeded}/{len(missing)} packages.")
+        print("Tool installed but may not work correctly without missing packages.")
+    else:
+        print(f"All {succeeded} system package(s) installed.")
diff --git a/src/cmdforge/tool.py b/src/cmdforge/tool.py
index fbb76a3..8ce5dc3 100644
--- a/src/cmdforge/tool.py
+++ b/src/cmdforge/tool.py
@@ -17,6 +17,54 @@ TOOLS_DIR = Path.home() / ".cmdforge"
 BIN_DIR = Path.home() / ".local" / "bin"
 
 
+@dataclass
+class SystemDependency:
+    """A system-level package dependency (apt, brew, pacman, etc.)."""
+    name: str
+    description: str = ""
+    binaries: List[str] = field(default_factory=list)  # Executables to check for
+    packages: dict = field(default_factory=dict)  # {apt: pkg, brew: pkg, ...}
+    _original_format: str = field(default="long", repr=False)  # Track for round-trip serialization
+
+    def to_dict(self):
+        """Serialize to dict or string (short form)."""
+        # Short form: if only name is set, return just the string
+        if self._original_format == "short" or (
+            not self.description and not self.binaries and not self.packages
+        ):
+            return self.name
+
+        d = {"name": self.name}
+        if self.description:
+            d["description"] = self.description
+        if self.binaries:
+            d["binaries"] = self.binaries
+        if self.packages:
+            d["packages"] = self.packages
+        return d
+
+    @classmethod
+    def from_dict(cls, data) -> "SystemDependency":
+        """Create from dict or string (short form)."""
+        if isinstance(data, str):
+            return cls(name=data, _original_format="short")
+        return cls(
+            name=data.get("name", ""),
+            description=data.get("description", ""),
+            binaries=data.get("binaries", []),
+            packages=data.get("packages", {}),
+            _original_format="long"
+        )
+
+    def get_binaries_to_check(self) -> List[str]:
+        """Return binaries to check, defaulting to [name]."""
+        return self.binaries if self.binaries else [self.name]
+
+    def get_package_name(self, pkg_manager: str) -> str:
+        """Return package name for a manager, defaulting to self.name."""
+        return self.packages.get(pkg_manager, self.name)
+
+
 @dataclass
 class ToolArgument:
     """Definition of a custom input argument."""
@@ -197,6 +245,7 @@ class Tool:
     steps: List[Step] = field(default_factory=list)
     output: str = "{input}"  # Output template
     dependencies: List[str] = field(default_factory=list)  # Required tools for meta-tools
+    system_dependencies: List[SystemDependency] = field(default_factory=list)  # System packages (apt, brew, etc.)
     source: Optional[ToolSource] = None  # Attribution for imported/external tools
     version: str = ""  # Tool version
     path: Optional[Path] = None  # Path to config.yaml (set by load_tool)
@@ -231,6 +280,12 @@ class Tool:
                 dependencies.append(dep["name"])
             # Skip invalid entries
 
+        # Parse system dependencies
+        raw_sys_deps = data.get("system_dependencies", [])
+        system_dependencies = []
+        for sd in raw_sys_deps:
+            system_dependencies.append(SystemDependency.from_dict(sd))
+
         return cls(
             name=data["name"],
             description=data.get("description", ""),
@@ -239,6 +294,7 @@ class Tool:
             steps=steps,
             output=data.get("output", "{input}"),
             dependencies=dependencies,
+            system_dependencies=system_dependencies,
             source=source,
             version=data.get("version", ""),
         )
@@ -258,6 +314,8 @@ class Tool:
             d["source"] = self.source.to_dict()
         if self.dependencies:
             d["dependencies"] = self.dependencies
+        if self.system_dependencies:
+            d["system_dependencies"] = [sd.to_dict() for sd in self.system_dependencies]
         d["arguments"] = [arg.to_dict() for arg in self.arguments]
         d["steps"] = [step.to_dict() for step in self.steps]
         d["output"] = self.output
@@ -271,9 +329,10 @@ class Tool:
         for arg in self.arguments:
             variables.append(arg.variable)
 
-        # Add step output variables
+        # Add step output variables (handle comma-separated output_var)
         for step in self.steps:
-            variables.append(step.output_var)
+            for var in step.output_var.split(','):
+                variables.append(var.strip())
 
         return variables
 
@@ -478,7 +537,7 @@ def create_wrapper_script(name: str) -> Path:
     script = f"""#!/bin/bash
 # CmdForge wrapper for '{name}'
 # Auto-generated - do not edit
-exec {python_path} -m cmdforge.runner {name} "$@"
+exec "{python_path}" -m cmdforge.runner "{name}" "$@"
 """
 
     wrapper_path.write_text(script)
diff --git a/tests/test_cli.py b/tests/test_cli.py
index 2739a06..8a62340 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -110,13 +110,14 @@ class TestCreateCommand:
         captured = capsys.readouterr()
         assert 'exists' in captured.err.lower() or 'exists' in captured.out.lower()
 
-    @pytest.mark.skip(reason="CLI does not yet validate tool names - potential enhancement")
     def test_create_invalid_name(self, temp_tools_dir, capsys):
         """Invalid tool name should fail."""
         with patch('sys.argv', ['cmdforge', 'create', 'invalid/name']):
             result = main()
 
         assert result != 0
+        captured = capsys.readouterr()
+        assert 'invalid' in captured.out.lower() or 'invalid' in captured.err.lower()
 
 
 class TestDeleteCommand:
diff --git a/tests/test_runner.py b/tests/test_runner.py
index de9acf6..8794a9f 100644
--- a/tests/test_runner.py
+++ b/tests/test_runner.py
@@ -92,6 +92,21 @@ Line 3: {var1} again"""
         result = substitute_variables("Count: {n}", {"n": 42})
         assert result == "Count: 42"
 
+    def test_zero_value_preserved(self):
+        """Zero should be preserved, not converted to empty string."""
+        result = substitute_variables("Count: {n}", {"n": 0})
+        assert result == "Count: 0"
+
+    def test_false_value_preserved(self):
+        """False should be preserved, not converted to empty string."""
+        result = substitute_variables("Enabled: {flag}", {"flag": False})
+        assert result == "Enabled: False"
+
+    def test_true_value_preserved(self):
+        """True should be preserved as 'True'."""
+        result = substitute_variables("Enabled: {flag}", {"flag": True})
+        assert result == "Enabled: True"
+
 
 class TestExecutePromptStep:
     """Tests for prompt step execution."""
@@ -179,9 +194,10 @@ class TestExecuteCodeStep:
         outputs, success = execute_code_step(step, variables)
 
         assert success is True
-        assert outputs["a"] == "1"
-        assert outputs["b"] == "2"
-        assert outputs["c"] == "3"
+        # Code step outputs preserve original types (integers here)
+        assert outputs["a"] == 1
+        assert outputs["b"] == 2
+        assert outputs["c"] == 3
 
     def test_code_uses_variables(self):
         step = CodeStep(
@@ -242,7 +258,43 @@ class TestExecuteCodeStep:
         outputs, success = execute_code_step(step, variables)
 
         assert success is True
-        assert outputs["result"] == "3"
+        # Code step outputs preserve original types (integer here)
+        assert outputs["result"] == 3
+
+    def test_code_preserves_complex_types(self):
+        """Code step outputs preserve lists/dicts for code→code workflows."""
+        step = CodeStep(
+            code="data = [1, 2, 3]\ninfo = {'key': 'value'}",
+            output_var="data, info"
+        )
+        variables = {"input": ""}
+
+        outputs, success = execute_code_step(step, variables)
+
+        assert success is True
+        assert outputs["data"] == [1, 2, 3]
+        assert outputs["info"] == {"key": "value"}
+
+    def test_code_to_code_workflow(self):
+        """Test that complex types can flow between code steps."""
+        # First step creates a list
+        step1 = CodeStep(
+            code="numbers = [1, 2, 3, 4, 5]",
+            output_var="numbers"
+        )
+        variables = {"input": ""}
+        outputs1, _ = execute_code_step(step1, variables)
+        variables.update(outputs1)
+
+        # Second step uses the list directly (no re-parsing needed)
+        step2 = CodeStep(
+            code="total = sum(numbers)",
+            output_var="total"
+        )
+        outputs2, success = execute_code_step(step2, variables)
+
+        assert success is True
+        assert outputs2["total"] == 15
 
 
 class TestRunTool:
diff --git a/tests/test_system_deps.py b/tests/test_system_deps.py
new file mode 100644
index 0000000..651dcea
--- /dev/null
+++ b/tests/test_system_deps.py
@@ -0,0 +1,310 @@
+"""Tests for system dependency management."""
+
+import shutil
+from unittest.mock import patch, MagicMock
+
+import pytest
+
+from cmdforge.tool import SystemDependency, Tool
+from cmdforge.system_deps import (
+    detect_os, detect_package_manager, check_system_dep,
+    get_install_command, get_install_command_string,
+    check_and_report, get_binary_path
+)
+
+
+class TestSystemDependencyDataclass:
+    """Tests for SystemDependency dataclass."""
+
+    def test_short_form_roundtrip(self):
+        """Short form 'ffmpeg' serializes back to string."""
+        dep = SystemDependency.from_dict("ffmpeg")
+        assert dep.name == "ffmpeg"
+        assert dep.to_dict() == "ffmpeg"
+
+    def test_long_form_roundtrip(self):
+        """Long form with all fields serializes correctly."""
+        data = {
+            "name": "ffmpeg",
+            "description": "Audio/video processing",
+            "binaries": ["ffplay", "ffmpeg"],
+            "packages": {"apt": "ffmpeg", "brew": "ffmpeg"}
+        }
+        dep = SystemDependency.from_dict(data)
+        result = dep.to_dict()
+
+        assert result["name"] == "ffmpeg"
+        assert result["description"] == "Audio/video processing"
+        assert result["binaries"] == ["ffplay", "ffmpeg"]
+        assert result["packages"]["apt"] == "ffmpeg"
+
+    def test_long_form_minimal_becomes_short(self):
+        """Long form with only name becomes short form on serialize."""
+        data = {"name": "curl"}
+        dep = SystemDependency.from_dict(data)
+        # Empty fields should serialize to short form
+        dep._original_format = "short"
+        assert dep.to_dict() == "curl"
+
+    def test_get_binaries_to_check_default(self):
+        """get_binaries_to_check returns [name] when binaries is empty."""
+        dep = SystemDependency(name="curl")
+        assert dep.get_binaries_to_check() == ["curl"]
+
+    def test_get_binaries_to_check_specified(self):
+        """get_binaries_to_check returns specified binaries."""
+        dep = SystemDependency(name="ffmpeg", binaries=["ffplay", "ffmpeg"])
+        assert dep.get_binaries_to_check() == ["ffplay", "ffmpeg"]
+
+    def test_get_package_name_default(self):
+        """get_package_name returns name when no override."""
+        dep = SystemDependency(name="ffmpeg")
+        assert dep.get_package_name("apt") == "ffmpeg"
+        assert dep.get_package_name("brew") == "ffmpeg"
+
+    def test_get_package_name_override(self):
+        """get_package_name returns override when specified."""
+        dep = SystemDependency(name="ffmpeg", packages={"brew": "ffmpeg-headless"})
+        assert dep.get_package_name("apt") == "ffmpeg"  # Default
+        assert dep.get_package_name("brew") == "ffmpeg-headless"  # Override
+
+
+class TestPlatformDetection:
+    """Tests for platform detection functions."""
+
+    @patch('platform.system')
+    def test_detect_os_linux(self, mock_system):
+        """detect_os returns 'linux' for Linux."""
+        mock_system.return_value = "Linux"
+        assert detect_os() == "linux"
+
+    @patch('platform.system')
+    def test_detect_os_darwin(self, mock_system):
+        """detect_os returns 'darwin' for macOS."""
+        mock_system.return_value = "Darwin"
+        assert detect_os() == "darwin"
+
+    @patch('platform.system')
+    def test_detect_os_windows(self, mock_system):
+        """detect_os returns 'windows' for Windows."""
+        mock_system.return_value = "Windows"
+        assert detect_os() == "windows"
+
+    @patch('cmdforge.system_deps.detect_os')
+    @patch('shutil.which')
+    def test_detect_package_manager_apt(self, mock_which, mock_os):
+        """detect_package_manager finds apt on Linux."""
+        mock_os.return_value = "linux"
+        mock_which.side_effect = lambda x: "/usr/bin/apt-get" if x == "apt-get" else None
+        assert detect_package_manager() == "apt"
+
+    @patch('cmdforge.system_deps.detect_os')
+    @patch('shutil.which')
+    def test_detect_package_manager_brew_macos(self, mock_which, mock_os):
+        """detect_package_manager finds brew on macOS."""
+        mock_os.return_value = "darwin"
+        mock_which.side_effect = lambda x: "/usr/local/bin/brew" if x == "brew" else None
+        assert detect_package_manager() == "brew"
+
+    @patch('cmdforge.system_deps.detect_os')
+    def test_detect_package_manager_windows_returns_none(self, mock_os):
+        """detect_package_manager returns None on Windows."""
+        mock_os.return_value = "windows"
+        assert detect_package_manager() is None
+
+
+class TestDependencyChecking:
+    """Tests for dependency checking functions."""
+
+    @patch('shutil.which')
+    def test_check_system_dep_found(self, mock_which):
+        """check_system_dep returns True when binary exists."""
+        mock_which.return_value = "/usr/bin/curl"
+        dep = SystemDependency(name="curl")
+        assert check_system_dep(dep) is True
+
+    @patch('shutil.which')
+    def test_check_system_dep_not_found(self, mock_which):
+        """check_system_dep returns False when binary not found."""
+        mock_which.return_value = None
+        dep = SystemDependency(name="nonexistent-pkg")
+        assert check_system_dep(dep) is False
+
+    @patch('shutil.which')
+    def test_check_system_dep_any_binary_satisfied(self, mock_which):
+        """Dep is satisfied if ANY binary is found."""
+        def which_side_effect(binary):
+            return "/usr/bin/ffplay" if binary == "ffplay" else None
+
+        mock_which.side_effect = which_side_effect
+        dep = SystemDependency(name="ffmpeg", binaries=["ffplay", "ffmpeg"])
+        assert check_system_dep(dep) is True
+
+    @patch('shutil.which')
+    def test_check_and_report(self, mock_which):
+        """check_and_report categorizes deps correctly."""
+        def which_side_effect(binary):
+            if binary in ["curl", "git"]:
+                return f"/usr/bin/{binary}"
+            return None
+
+        mock_which.side_effect = which_side_effect
+
+        deps = [
+            SystemDependency(name="curl"),
+            SystemDependency(name="git"),
+            SystemDependency(name="nonexistent"),
+        ]
+
+        installed, missing = check_and_report(deps)
+
+        assert len(installed) == 2
+        assert len(missing) == 1
+        assert missing[0].name == "nonexistent"
+
+
+class TestInstallCommands:
+    """Tests for install command generation."""
+
+    def test_get_install_command_apt(self):
+        """get_install_command returns correct apt command."""
+        dep = SystemDependency(name="ffmpeg")
+        cmd = get_install_command(dep, "apt")
+        assert cmd == ["sudo", "apt-get", "install", "-y", "ffmpeg"]
+
+    def test_get_install_command_brew(self):
+        """get_install_command returns correct brew command."""
+        dep = SystemDependency(name="ffmpeg")
+        cmd = get_install_command(dep, "brew")
+        assert cmd == ["brew", "install", "ffmpeg"]
+
+    def test_get_install_command_pacman(self):
+        """get_install_command returns correct pacman command."""
+        dep = SystemDependency(name="ffmpeg")
+        cmd = get_install_command(dep, "pacman")
+        assert cmd == ["sudo", "pacman", "-S", "--noconfirm", "ffmpeg"]
+
+    def test_get_install_command_dnf(self):
+        """get_install_command returns correct dnf command."""
+        dep = SystemDependency(name="ffmpeg")
+        cmd = get_install_command(dep, "dnf")
+        assert cmd == ["sudo", "dnf", "install", "-y", "ffmpeg"]
+
+    def test_get_install_command_unknown_manager(self):
+        """get_install_command returns None for unknown manager."""
+        dep = SystemDependency(name="ffmpeg")
+        cmd = get_install_command(dep, "unknown")
+        assert cmd is None
+
+    def test_install_command_no_shell_injection(self):
+        """Install command uses list, no shell injection possible."""
+        # Even malicious input is safe because subprocess with list doesn't use shell
+        dep = SystemDependency(name="test; rm -rf /")
+        cmd = get_install_command(dep, "apt")
+        assert cmd == ["sudo", "apt-get", "install", "-y", "test; rm -rf /"]
+        # This is safe - the semicolon is passed as literal arg, not interpreted
+
+    def test_get_install_command_string(self):
+        """get_install_command_string returns readable string."""
+        dep = SystemDependency(name="ffmpeg")
+        cmd_str = get_install_command_string(dep, "apt")
+        assert cmd_str == "sudo apt-get install -y ffmpeg"
+
+
+class TestToolIntegration:
+    """Tests for Tool integration with system dependencies."""
+
+    def test_tool_with_system_dependencies_loads(self):
+        """Tool config with system_dependencies parses correctly."""
+        data = {
+            "name": "test-tool",
+            "description": "Test",
+            "system_dependencies": [
+                "curl",
+                {
+                    "name": "ffmpeg",
+                    "description": "Audio processing",
+                    "binaries": ["ffplay"],
+                }
+            ],
+            "steps": [],
+            "output": "{input}"
+        }
+
+        tool = Tool.from_dict(data)
+
+        assert len(tool.system_dependencies) == 2
+        assert tool.system_dependencies[0].name == "curl"
+        assert tool.system_dependencies[1].name == "ffmpeg"
+        assert tool.system_dependencies[1].binaries == ["ffplay"]
+
+    def test_tool_to_dict_includes_system_dependencies(self):
+        """Tool.to_dict includes system_dependencies when present."""
+        tool = Tool(
+            name="test-tool",
+            description="Test",
+            system_dependencies=[
+                SystemDependency(name="curl", _original_format="short"),
+                SystemDependency(
+                    name="ffmpeg",
+                    description="Audio",
+                    binaries=["ffplay"],
+                    _original_format="long"
+                )
+            ]
+        )
+
+        data = tool.to_dict()
+
+        assert "system_dependencies" in data
+        assert len(data["system_dependencies"]) == 2
+        assert data["system_dependencies"][0] == "curl"  # Short form
+        assert data["system_dependencies"][1]["name"] == "ffmpeg"  # Long form
+
+    def test_tool_without_system_dependencies(self):
+        """Tool without system_dependencies works correctly."""
+        data = {
+            "name": "simple-tool",
+            "description": "Test",
+            "steps": [],
+            "output": "{input}"
+        }
+
+        tool = Tool.from_dict(data)
+        assert tool.system_dependencies == []
+
+        # to_dict should not include empty system_dependencies
+        result = tool.to_dict()
+        assert "system_dependencies" not in result
+
+
+class TestRunnerIntegration:
+    """Tests for runner.py integration."""
+
+    @patch('cmdforge.system_deps.check_system_dep')
+    def test_check_system_dependencies_function(self, mock_check):
+        """check_system_dependencies returns missing deps."""
+        from cmdforge.runner import check_system_dependencies
+
+        mock_check.side_effect = lambda d: d.name != "missing-pkg"
+
+        tool = Tool(
+            name="test-tool",
+            system_dependencies=[
+                SystemDependency(name="installed-pkg"),
+                SystemDependency(name="missing-pkg"),
+            ]
+        )
+
+        missing = check_system_dependencies(tool)
+
+        assert len(missing) == 1
+        assert missing[0].name == "missing-pkg"
+
+    def test_check_system_dependencies_empty(self):
+        """check_system_dependencies returns empty for no deps."""
+        from cmdforge.runner import check_system_dependencies
+
+        tool = Tool(name="test-tool")
+        missing = check_system_dependencies(tool)
+        assert missing == []